Robust test method for time-course microarray experiments

BMC Bioinformatics

Methodology Article

Insuk Sohn¹  Sin-Ho Jung²  Kouros Owzar²  Stephen L George²  Sujong Kim³ 

[1] Biostatistics and Bioinformatics Center, Samsung Cancer Research Institute, Samsung Medical Center, 137-710, Seoul, Republic of Korea;CALGB Statistical Center, 27710, NC, USA;Department of Biostatistics and Bioinformatics, Duke University Medical Center, 27710, NC, USA;CALGB Statistical Center, 27710, NC, USA;R&D Center, Komipharm International Co., LTD, 429-450, Kyounggi-do, Republic of Korea;

关键词: Quantile Regression;    Prognostic Gene;    Extensive Simulation Study;    Outlier Effect;    Multiple Testing Procedure;   

DOI  :  10.1186/1471-2105-11-391

 received in 2010-03-08, accepted in 2010-07-22,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundIn a time-course microarray experiment, the expression level for each gene is observed across a number of time-points in order to characterize the temporal trajectories of the gene-expression profiles. For many of these experiments, the scientific aim is the identification of genes for which the trajectories depend on an experimental or phenotypic factor. There is an extensive recent body of literature on statistical methodology for addressing this analytical problem. Most of the existing methods are based on estimating the time-course trajectories using parametric or non-parametric mean regression methods. The sensitivity of these regression methods to outliers, an issue that is well documented in the statistical literature, should be of concern when analyzing microarray data.ResultsIn this paper, we propose a robust testing method for identifying genes whose expression time profiles depend on a factor. Furthermore, we propose a multiple testing procedure to adjust for multiplicity.ConclusionsThrough an extensive simulation study, we will illustrate the performance of our method. Finally, we will report the results from applying our method to a case study and discussing potential extensions.

【 授权许可】

CC BY   
© Sohn et al; licensee BioMed Central Ltd. 2010